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WASHINGTON — Ambitious legislation to stanch the growing number of sexual assaults in the armed forces by overhauling the military justice system faces an uncertain future due to vigorous objections from senior Defense Department leaders and key members of Congress who are concerned the proposed changes go too far.

The bill crafted by Sen. Kirsten Gillibrand, D-N.Y., cleared an important hurdle Tuesday when the Senate Armed Services personnel subcommittee that she chairs approved the measure. But the legislation must get through the full committee and its chairman, Sen. Carl Levin, D-Mich., has signaled his intent to offer an alternative that would mute the most aggressive reforms in Gillibrand’s bill.

Gillibrand’s legislation would remove commanders from the process of deciding whether serious crimes, including sexual misconduct cases, go to trial. That judgment would rest instead with seasoned trial lawyers who have prosecutorial experience and hold the rank of colonel or above. Her bill also would take away a commander’s authority to convene a court-martial. That responsibility would be given to new and separate offices outside the victim’s chain of command.

But Levin and other lawmakers, echoing fears voiced by the Joint Chiefs of Staff, believe that cutting commanders out of the legal process would undermine their ability to enforce good order and discipline within the ranks.

“Commanders ought to have and use the tools that are the most effective in terms of changing climate and affecting the behavior of people in their units, and that’s to have available to them the power to send to a court-martial,” Levin said Monday.

The Armed Services Committee is scheduled to meet Wednesday to vote on the provisions that will be included in a sweeping defense policy bill for the 2014 fiscal year that begins Oct. 1.

Levin’s alternative, which has bipartisan support, would require a review by an individual higher in the chain of command if a commander decides not to prosecute a sexual assault case. It would make it a crime to retaliate against victims who report a sexual assault and relieve commanders of their responsibilities if they do not create a climate receptive for victims who report crimes.

Sen. Lindsey Graham, R-S.C., the personnel subcommittee’s top Republican, said commanders shouldn’t be sidelined from sexual assault cases. He and Sen. Roy Blunt, R-Mo., both voted against Gillibrand’s legislation, which the panel passed by voice vote.

“I don’t think you quite resolve a problem in the military without the chain of command buying into it and being held more accountable,” Graham said.

But frustration over the Defense Department’s failure so far to change the military’s male-dominated culture and eradicate sexual assaults is driving support for substantive changes.

Sen. Barbara Boxer, D-Calif., a cosponsor of Gillibrand’s legislation, said in a statement that she was “stunned” to learn of Levin’s alternative. Several U.S. allies have already taken serious cases outside the chain of command, Boxer said, and the committee should follow suit.

“Instead of embracing a broken system, the full committee should pass the reforms backed by the subcommittee that emulate our allies in Israel, Great Britain, Australia and Canada,” Boxer said.

The chairman of the Senate Judiciary Committee said Tuesday at a separate hearing that Congress is considering stripping the military of its authority to prosecute sexual assault cases and shifting the responsibility to state prosecutors.

Sen. Patrick Leahy, D-Vt., told Defense Secretary Chuck Hagel and Army Gen. Martin Dempsey, the chairman of the Joint Chiefs of Staff, that the status quo is unacceptable.

Leahy said that while the proposal is controversial, it would send a message to commanders that doing “things as they’ve always been done is not acceptable.”

Hagel assured Leahy that changes will be made to deal with sexual assaults in the services and specifically mentioned a specially appointed panel that would be meeting in two weeks to consider reforms.

“There are going to have to be changes made. There will be changes made,” Hagel told the Senate Appropriations defense subcommittee. “But as we make those changes and work with the Congress on this, we need to be as sure as we can be that the consequences that will come from whatever decisions made by the Congress to make those kinds of adjustments that we need to make — and you know I agree with that in many ways — that they’re thoughtful.”

The Pentagon estimated in a recent report that as many as 26,000 military members may have been sexually assaulted last year, up from an estimated 19,000 assaults in 2011, based on an anonymous survey of military personnel. While the number of sexual assaults that members of the military actually reported rose 6 percent to 3,374 in 2012, thousands of victims were still unwilling to come forward despite new oversight and assistance programs aimed at curbing the crimes, the report said.

By week’s end, the House is scheduled to vote on its version of a defense policy bill that would take away the power of military commanders to overturn convictions in rape and assault cases.

The change was initially recommended in April by Defense Secretary Chuck Hagel and is backed by Dempsey, the service chiefs and many members of the House and Senate.

The legislation approved last week by the House Armed Services Committee currently requires that anyone found guilty of rape, sexual assault, forcible sodomy or an attempt to commit any of those offenses receive a punishment that includes dismissal from military service or a dishonorable discharge.

Rep. Michael Turner, R-Ohio, plans to offer an amendment to the House bill during floor debate that would make two years of confinement and a dishonorable discharge the mandatory minimum sentence for any service member convicted of rape or sexual assault. Imposing a tough, minimum sentence will serve as a deterrent to help prevent sexual assaults, according to Turner.

The House legislation eliminates the five-year statute of limitations on trial by court-martial for sexual assault and sexual assault of a child. It also establishes the authority for military legal counsel to provide legal assistance to victims of sex-related offenses and requires enhanced training for all military and civilian attorneys involved in sex-related cases.

Gillibrand’s legislation also includes provisions from sexual assault prevention bills. It requires all the military branches to provide any victims with a special military lawyer who would assist them throughout the process, a measure first offered by Sens. Patty Murray, D-Wash., and Kelly Ayotte, R-N.H.

Her bill also has a measure crafted by Sens. Amy Klobuchar, D-Minn., and Lisa Murkowski, R-Alaska, requiring that substantiated sex-related offenses be noted in the personnel records of the offenders.